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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 14-57274732-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=57274732&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 57274732,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018229.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.563C>A",
"hgvs_p": "p.Ser188Tyr",
"transcript": "NM_018229.4",
"protein_id": "NP_060699.3",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 490,
"cds_start": 563,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261558.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018229.4"
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.563C>A",
"hgvs_p": "p.Ser188Tyr",
"transcript": "ENST00000261558.8",
"protein_id": "ENSP00000261558.3",
"transcript_support_level": 1,
"aa_start": 188,
"aa_end": null,
"aa_length": 490,
"cds_start": 563,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018229.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261558.8"
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.605C>A",
"hgvs_p": "p.Ser202Tyr",
"transcript": "ENST00000431972.6",
"protein_id": "ENSP00000390531.2",
"transcript_support_level": 2,
"aa_start": 202,
"aa_end": null,
"aa_length": 504,
"cds_start": 605,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000431972.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "n.954C>A",
"hgvs_p": null,
"transcript": "ENST00000554931.1",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000554931.1"
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.563C>A",
"hgvs_p": "p.Ser188Tyr",
"transcript": "ENST00000854558.1",
"protein_id": "ENSP00000524617.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 466,
"cds_start": 563,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854558.1"
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.563C>A",
"hgvs_p": "p.Ser188Tyr",
"transcript": "ENST00000921974.1",
"protein_id": "ENSP00000592033.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 414,
"cds_start": 563,
"cds_end": null,
"cds_length": 1245,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921974.1"
},
{
"aa_ref": "S",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.605C>A",
"hgvs_p": "p.Ser202Tyr",
"transcript": "XM_011536940.4",
"protein_id": "XP_011535242.1",
"transcript_support_level": null,
"aa_start": 202,
"aa_end": null,
"aa_length": 504,
"cds_start": 605,
"cds_end": null,
"cds_length": 1515,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536940.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.74+5344C>A",
"hgvs_p": null,
"transcript": "ENST00000854559.1",
"protein_id": "ENSP00000524618.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 152,
"cds_start": null,
"cds_end": null,
"cds_length": 459,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854559.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "n.74+5344C>A",
"hgvs_p": null,
"transcript": "ENST00000555448.5",
"protein_id": "ENSP00000451306.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000555448.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "n.418+5344C>A",
"hgvs_p": null,
"transcript": "NR_026895.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_026895.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"hgvs_c": "c.*9C>A",
"hgvs_p": null,
"transcript": "ENST00000556995.1",
"protein_id": "ENSP00000452211.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 245,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556995.1"
}
],
"gene_symbol": "AP5M1",
"gene_hgnc_id": 20192,
"dbsnp": "rs984970036",
"frequency_reference_population": 0.00001982556,
"hom_count_reference_population": 0,
"allele_count_reference_population": 32,
"gnomad_exomes_af": 0.0000212056,
"gnomad_genomes_af": 0.00000657039,
"gnomad_exomes_ac": 31,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.42476075887680054,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.161,
"revel_prediction": "Benign",
"alphamissense_score": 0.1287,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.894,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018229.4",
"gene_symbol": "AP5M1",
"hgnc_id": 20192,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.563C>A",
"hgvs_p": "p.Ser188Tyr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}